[gmx-users] Martini with PME, temp two low

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Apr 25 13:10:45 CEST 2013


Hello all, 

I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to  290 K. Below my *.mdp parameters for a NPT equil at 298K 


integrator               = md
dt                       = 0.020
nsteps                   = 10000 ; 200ps
nstcomm                  = 10
comm-grps        =
;refcoord_scaling         = com

nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 100
;nstxtcout                = 1000
xtc_precision            = 100
;xtc-grps                 =
energygrps               = AOT W ION OCT

nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.

; PME parameters
coulombtype              = PME
rcoulomb                 = 1.2
rvdw                     = 1.2
fourierspacing           = 0.12
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
pme_order                = 4

tcoupl                   = v-rescale
tc-grps                  = AOT_W_ION OCT
tau_t                    = 1.0 1.0
ref_t                    = 298 298
Pcoupl                   = berendsen
Pcoupltype               = isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

;gen_vel                  = no
;gen_temp                 = 0
;gen_seed                 = 473529


; MARTINI and CONSTRAINTS
; for ring systems and stiff bonds constraints are defined
; which are best handled using Lincs.

constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_warnangle          = 3


Results obtained with W/ PME 

   Statistics over 10001 steps using 1001 frames

   Energies (kJ/mol)
           Bond       G96Angle        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.63789e+04    1.25195e+03   -4.02093e+05   -8.22079e+03   -4.86843e+04
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -4.41367e+05    7.81801e+04   -3.63187e+05    2.90373e+02   -1.76470e+01
    T-AOT_W_ION          T-OCT
    2.90629e+02    2.90357e+02

Results W:o PME

   Energies (kJ/mol)
           Bond       G96Angle        LJ (SR)   Coulomb (SR)      Potential
    1.60482e+04    1.24820e+03   -3.34608e+05   -7.33665e+02   -3.18046e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    8.02685e+04   -2.37777e+05    2.98129e+02   -3.07123e+01

          Box-X          Box-Y          Box-Z
    1.52926e+01    1.52926e+01    1.52926e+01


    T-AOT_W_ION          T-OCT
    2.98141e+02    2.98129e+02


Did I miss something ?


Note that for the moment i do not use the polarizable water model.

Thanks for your help 

Stephane







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